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--- evoss [2018/07/19 22:57] – sean
+++ evoss [2018/10/30 15:41] (current) – removed sean
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-==== Evolu-sec package ====
-<html>
-<p class=MsoNormal style='text-align:justify;text-justify:inter-ideograph'><span
-class=SpellE><span lang=EN-GB>Evolu</span></span><span lang=EN-GB>-sec package
-is a part of research project as “Modelling the evolution of protein secondary
-structure: a new phylogenetic metric suitable for assessing structural
-similarity”.<o:p></o:p></span></p>
-<p class=MsoNormal style='text-align:justify;text-justify:inter-ideograph'><span
-class=SpellE><span lang=EN-GB>Evolu</span></span><span lang=EN-GB>-sec package
-contains phylogenetic analysis tools based on an evolutionary model of
-secondary structure <b style='mso-bidi-font-weight:normal'>[centre, Table 1]</b>.
-Analysis focus on phylogenetic tree inference <b style='mso-bidi-font-weight:
-normal'>[left]</b>, evolutionary distance estimation <b style='mso-bidi-font-weight:
-normal'>[top]</b>, and ancestral secondary structure reconstruction. The research project abstract is provided in next session. <b
-style='mso-bidi-font-weight:normal'>[bottom and right]</b>.</span></p>
-</html>
-The dataset for the model development and the software can be accessed in the [[http://bioinf.scmb.uq.edu.au/evoss#supplementary_data|“Supplementary Data”]] session.
-{{:research:evolusec.png}}
-\\
-----
-==== Research Project ====
-**Modelling the evolution of protein secondary structure: a new phylogenetic metric suitable for assessing structural similarity**\\
-[[http://bioinf.scmb.uq.edu.au/research/jhih_siang_sean_lai|Jhih-Siang Lai]], [[https://www.rostlab.org/|Burkhard Rost
-]], [[http://kobelab.biosci.uq.edu.au/wiki/|Bostjan Kobe]] and [[http://bioinf.scmb.uq.edu.au/research/mikael_boden|Mikael Bodén]]\\
-[[http://www.scmb.uq.edu.au/|School of Chemistry and Molecular Biosciences]], [[http://www.uq.edu.au|The University of Queensland]]\\
-Contact: //[[js.lai@uqconnect.edu.au|Jhih-Siang Lai]]//
-**Abstract**\\
-<html>
-<p class=MsoNormal style='text-align:justify;text-justify:inter-ideograph'><a
-name="_GoBack"></a><span lang=EN-GB>Ancestral sequence reconstruction has had
-recent success in decoding the origins and the determinants of complex protein
-functions. However, attempts to reconstruct ancient proteins and phylogenetic
-analyses of remote homologues must handle extreme amino-acid sequence diversity
-resulting from extended periods of evolutionary change. We exploited the wealth
-of protein structures in the Protein Data Bank (PDB) to develop an evolutionary
-model based on protein secondary structure. The approach follows the
-differences between discrete secondary structure states observed in modern
-proteins and those hypothesised in their immediate ancestors. Based on this new
-evolutionary model, we implemented maximum likelihood-based phylogenetic
-inference tools to reconstruct ancestral secondary structure. The predictive
-accuracy from the use of the evolutionary model surpasses that of structure
-comparative modelling and sequence-based prediction methods; the reconstruction
-extracts information not available from modern structures or the ancestral
-protein sequences alone. Based on a phylogenetic analysis of a sequence-diverse
-protein family, we showed that the model has the capacity to highlight
-relationships that are evolutionarily rooted in structure and not evident in
-sequence-based phylogenetic analysis.</span></p>
-</html>
-----
-==== Supplementary Data ====
-Supplementary data for "**Modelling the evolution of protein secondary structure: a new phylogenetic metric suitable for assessing structural similarity**" can be downloaded as\\ [[https://cloudstor.aarnet.edu.au/plus/index.php/s/lxuMi0nwv8mRuov|Dataset]] or [[https://cloudstor.aarnet.edu.au/plus/index.php/s/MbQRrsIp1txz27a|Software]], separately.\\
-\\
-Package may be downloaded as single one archive as\\ [[https://cloudstor.aarnet.edu.au/plus/index.php/s/UgZbhzrNcgQtMkQ|Full package download]].\\
-[[Research:Package_content|Package contents can be viewed here.]]\\
-[[https://cloudstor.aarnet.edu.au/plus/index.php/s/m17DG77S1dVK0cF|Supplementary document]]
-\\
-  * (Ancestral secondary structure reconstruction) ASSR needs version MATLAB 8.2 (R2013b) or later.\\
-  * Please feedback needs to the [[js.lai@uqconnect.edu.au|author]].
-----
-==== References ====
-<html>
-<body bgcolor=white lang=ZH-TW link=blue vlink="#954F72" style='tab-interval:
-.0pt;text-justify-trim:punctuation'>
-<div class=WordSection1 style='layout-grid:20.0pt'>
-<p class=MsoListParagraph style='margin-left:18.0pt;mso-para-margin-left:0gd;
-text-align:justify;text-justify:inter-ideograph;text-indent:-18.0pt;mso-list:
-l0 level1 lfo1'><![if !supportLists]><span lang=EN-US style='font-size:10.0pt;
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-mso-bidi-font-family:Arial;color:#2E2E2E;mso-font-kerning:0pt;mso-ansi-language:
-EN-US'>Dayhoff M, Schwartz R and <span class=SpellE>Orcutt</span> B
-(1978),&nbsp;<i>&quot;A Model of Evolutionary Change in Proteins&quot;</i>, In
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-<p class=MsoListParagraph style='margin-left:18.0pt;mso-para-margin-left:0gd;
-text-align:justify;text-justify:inter-ideograph;text-indent:-18.0pt;mso-list:
-l0 level1 lfo1'><![if !supportLists]><span lang=EN-US style='font-size:10.0pt;
-font-family:"Helvetica",sans-serif;mso-fareast-font-family:Helvetica;
-mso-bidi-font-family:Helvetica;color:#2E2E2E;mso-font-kerning:0pt;mso-ansi-language:
-EN-US'><span style='mso-list:Ignore'>2.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
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-style='font-size:10.0pt;font-family:"Helvetica",sans-serif;mso-fareast-font-family:
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-EN-US'> T, Williams SJ and Kobe B (2015),&nbsp;<i>&quot;Structure and function
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-<p class=MsoListParagraph style='margin-left:18.0pt;mso-para-margin-left:0gd;
-text-align:justify;text-justify:inter-ideograph;text-indent:-18.0pt;mso-list:
-l0 level1 lfo1'><![if !supportLists]><span lang=EN-US style='font-size:10.0pt;
-font-family:"Helvetica",sans-serif;mso-fareast-font-family:Helvetica;
-mso-bidi-font-family:Helvetica;color:#2E2E2E;mso-font-kerning:0pt;mso-ansi-language:
-EN-US'><span style='mso-list:Ignore'>3.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
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-EN-US'>Clifton BE and Jackson CJ (2016),&nbsp;<i>&quot;Ancestral Protein
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-Vol. 23(2), pp. 236-245.<o:p></o:p></span></p>
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-text-align:justify;text-justify:inter-ideograph;text-indent:-18.0pt;mso-list:
-l0 level1 lfo1'><![if !supportLists]><span lang=EN-US style='font-size:10.0pt;
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-mso-bidi-font-family:Helvetica;color:#2E2E2E;mso-font-kerning:0pt;mso-ansi-language:
-EN-US'><span style='mso-list:Ignore'>4.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
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-EN-US'>Hudson WH, <span class=SpellE>Kossmann</span> BR, de Vera IM, Chuo SW, <span
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-EA (2016),&nbsp;<i>&quot;Distal substitutions drive divergent DNA specificity
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-l0 level1 lfo1'><![if !supportLists]><span lang=EN-US style='font-size:10.0pt;
-font-family:"Helvetica",sans-serif;mso-fareast-font-family:Helvetica;
-mso-bidi-font-family:Helvetica;color:#2E2E2E;mso-font-kerning:0pt;mso-ansi-language:
-EN-US'><span style='mso-list:Ignore'>5.<span style='font:7.0pt "Times New Roman"'>&nbsp;&nbsp;&nbsp;&nbsp;
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-font-family:"Helvetica",sans-serif;mso-fareast-font-family:"Times New Roman";
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-EN-US'>Wilson C, <span class=SpellE>Agafonov</span> RV, <span class=SpellE>Hoemberger</span>
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-J, <span class=SpellE>Buosi</span> V, <span class=SpellE>Otten</span> R,
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-(6224), pp. 882-886.<o:p></o:p></span></p>
-</div>
-</body>
-</html>
-----
-==== External links ====
-[[https://www.researchgate.net/profile/Jhih_Siang_Lai|Sean in ResearchGate]]\\
-[[research:jhih_siang_sean_lai|Sean's profile]]\\
-Last updated by --- //[[js.lai@uqconnect.edu.au|Jhih-Siang Lai]] 2017/07/11 21:53//